ENST00000494869.2:n.632+19888T>C

Variant names:

• chr3-120387973-T-C
• rs1733329
• ENST00000494869.2:n.632+19888T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494869.2(BTNL12P):​n.632+19888T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,122 control chromosomes in the GnomAD database, including 45,429 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.77 (45400 hom., cov: 30)
  • Exomes 𝑓: 0.70 (29 hom.)
• Consequence: BTNL12P ENST00000494869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 6 publications found

Genes affected

BTNL12P (HGNC:):

BTNL12P (HGNC:52935): (butyrophilin like 12, pseudogene)

PPDPFP1 (HGNC:56491): (PPDPF pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTNL12P	NR_187254.1	n.996+19888T>C		intron_variant	Intron 3 of 4
BTNL12P	NR_187255.1	n.996+19888T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTNL12P	ENST00000494869.2	n.632+19888T>C		intron_variant	Intron 3 of 4	5
BTNL12P	ENST00000635496.2	n.180+19888T>C		intron_variant	Intron 1 of 2	5
BTNL12P	ENST00000732430.1	n.185+19888T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116220 AN: 151896 Hom.: 45332 Cov.: 30

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.724

GnomAD4 exome AF: 0.704 AC: 76 AN: 108 Hom.: 29 AF XY: 0.633 AC XY: 38 AN XY: 60

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.733 AC: 22 AN: 30

European-Finnish (FIN) AF: 0.786 AC: 11 AN: 14

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.679 AC: 38 AN: 56

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.765 AC: 116347 AN: 152014 Hom.: 45400 Cov.: 30 AF XY: 0.765 AC XY: 56805 AN XY: 74296

African (AFR) AF: 0.931 AC: 38656 AN: 41516

American (AMR) AF: 0.687 AC: 10496 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2138 AN: 3462

East Asian (EAS) AF: 0.818 AC: 4214 AN: 5152

South Asian (SAS) AF: 0.803 AC: 3858 AN: 4802

European-Finnish (FIN) AF: 0.692 AC: 7309 AN: 10560

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47381 AN: 67928

Other (OTH) AF: 0.725 AC: 1532 AN: 2112

Alfa AF: 0.725 Hom.: 26313

Bravo AF: 0.770

Asia WGS AF: 0.825 AC: 2872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1733329; hg19: chr3-120106820;